OR they could have given Harry a fabulous arc.
Harry could have really been an alien like they wanted us to believe in Favorite Son, only instead of being bullshit it could have been real and Harry has to make his big decision and he stays with the ship only he is full of extra angst because of leaving his biological people behind. So much angst Janeway rips him a new clarinet hole.
Harry could be a sleeper agent for Section 31 and it takes us three seasons to find out because stuff keeps happening but even Harry doesn't know he's a sleeper agent until some alien probe activates him.
And of course there's my favorite suggestion which is the time Harry gestated 7 and Janeway's baby for them so they didn't miss a day of work.
The Harry arcs write themselves!